Re: [AMBER] Clustering problem

From: Lorenzo Gontrani <>
Date: Wed, 17 Sep 2014 14:56:15 +0200

grave grezza!!hai scritto xtc amber,ma il formato xtc รจ di gromacs!!come
dire comunista a Berlusconi..
Il giorno 17/set/2014 13:43, "Alessandro Mariani" <> ha scritto:

> Hello,
> I'm currently having some problems and maybe you can help me.
> I have a MD trajectory (Amber xtc) where are visible some solute clusters.
> The thing I want to do is to identify these clusters (i. e. which molecules
> are part of it) and then compute the lifetime of them (as an
> autocorrelation function). The criterion of two molecules to be in the same
> cluster is that their centre of mass are within a certain distance.
> I'm asking if there is a method, to identify a solute cluster using the
> criterion of center of mass pair distance. If there is a ready-to-use tool
> to do it, it will be great, but there will be no problem even if I'll have
> to write it. I have some programming skills, I would say average, in C and
> C++. In the attachments you will find a pseudo-program (no programming
> language) that I was writing to solve this problem, but it has some
> problems. The other file is a practical example of the program.
> Regards
> _____________________________________________
> Dr. Alessandro Mariani
> PhD Student
> Department of Chemistry
> "La Sapienza" University of Rome
> P.le Aldo Moro, 5
> 00185 Rome (IT)
> Telephone: +39 06 49934082
> Mobile Phone: +39 340 4124911
> _____________________________________________
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Wed Sep 17 2014 - 06:00:06 PDT
Custom Search